Abstract:
:Binding interactions of the phenazinium dye Janus green blue (JGB) with human and bovine serum albumins (BSA - and BSA) have been explored for the first time from multi-spectroscopic and calorimetric measurements aided by in silico calculations. The formation of ground state complexes between JGB and the respective serum albumins have been suggested from the UV-Vis and steady-state fluorescence spectroscopic studies. The nonlinear Stern Volmer (SV) plots at higher concentrations of JGB primarily indicate the formation of more than one ground state complexes in BSA -/BSA-JGB systems. Modified SV plots and isothermal titration calorimetry (ITC) studies however signify the possibilities of one type of binding complexes between HSA/BSA - JGB systems. Binding constants and the thermodynamic parameters associated with the HSA/BSA-JGB complexes have also been estimated from the ITC studies. Förster distances (R0 ) for HSA-JGB and BSA-JGB complexes are estimated from Förster resonance energy transfer (FRET) results. Variations in the micro-environment of the Tyr and Trp residues of the serum proteins in presence of JGB have been observed from the synchronous fluorescence measurements. The conformational changes in the protein structures induced by the dye JGB have been revealed from 3 D fluorescence and circular dichroism (CD) studies. The experimental observations are supported by in silico calculations. This in depth investigation on the interactions of serum albumins with JGB may provide the fundamental information toward exploring the therapeutic efficacy of JGB as a potent drug molecule. Communicated by Ramaswamy H. Sarma.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Saha S,Bhattacharjee S,Chowdhury Jdoi
10.1080/07391102.2020.1870156subject
Has Abstractpub_date
2021-01-07 00:00:00pages
1-17eissn
0739-1102issn
1538-0254pub_type
杂志文章abstract::Transcription factor NAM-B1 has a major role in the process of senescence, which results in higher Fe and Zn concentrations in grains of wild wheat (T. durum; Td). The absence of the wild type NAMB1 in T. aestivum (Ta), one of the cardinal crops essential for more than 1/3rd of the global population, affects Fe and Zn...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1680435
更新日期:2020-08-01 00:00:00
abstract::Communicated by Ramaswamy H. Sarma. ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 信件
doi:10.1080/07391102.2019.1688193
更新日期:2020-10-01 00:00:00
abstract::For almost 50 years the conclusive explanation of Chargaff's second parity rule (CSPR), the equality of frequencies of nucleotides A=T and C=G or the equality of direct and reverse complement trinucleotides in the same DNA strand, has not been determined yet. Here, we relate CSPR to the interstrand mirror symmetry in ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
doi:10.1080/07391102.2015.1080628
更新日期:2016-07-01 00:00:00
abstract::BCR-ABL fusion protein drives chronic myeloid leukemia (CML) which constitutively activates tyrosine kinase involved in the initiation and maintenance of CML phenotype. Ponatinib, an oral drug, was discovered as an efficient BCR-ABL inhibitor by addressing imatinib drug resistance arising due to the point mutations at...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1559765
更新日期:2019-11-01 00:00:00
abstract::Tris-intercalation of an acridine trimer into the self-complementary dodecanucleotide d(CTTCGCGCGAAG) has been studied, in solution, by means of 1H and 31P nuclear magnetic resonance. In a first step all the non-exchangeable protons (except H5', H5"), the imino protons and seven of the eleven phosphorus have been assi...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1988.10506498
更新日期:1988-12-01 00:00:00
abstract::Crystalline complexes of yeast tRNA(phe) and the oligopeptide antibiotics netropsin and distamycin A were prepared by diffusing drugs into crystals of tRNA. X-ray structure analyses of these complexes reveal a single common binding site for both drugs which is located in the major or deep groove of the tRNA T-stem. Th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1984.10507555
更新日期:1984-08-01 00:00:00
abstract::It has been found that DNA molecules are often hooked around obstacles in a U-shaped configuration in gel electrophoresis. To understand the dynamics of the unhooking of U-shaped DNA molecules undergoing gel electrophoresis, we have examined the length changes of the longer and shorter arms of the U-shape as a functio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1991.10507895
更新日期:1991-08-01 00:00:00
abstract::The potassium channel Kv1.3 is an important pharmacological target and the Kaliotoxin-type toxins (α-KTX-3 family) are its specific blockers. Here, we study the binding process of two kinds of Kaliotoxin-type toxins:BmKTX and its mutant (BmKTX-D33H) toward to Kv1.3 channel using MD simulation and umbrella sampling sim...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1760135
更新日期:2020-05-06 00:00:00
abstract::A theoretical study is presented of the energetic and structural properties of covalent adducts of benzo[a]pyrene and a DNA fragment. Energy optimisation is performed with the use of minimiser with constraints and an advanced semiempirical energy formula. Three types of adducts are studied: an external complex with th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1987.10507682
更新日期:1987-04-01 00:00:00
abstract::Regulation of gene expression in eukaryotes involves a complex assembly of DNA recognition sequence elements and their respective protein factors. The upstream promoter/enhancer sequences are position and orientation independent. Despite their variable distances from the TATA box and transcription start site, interact...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507988
更新日期:1992-06-01 00:00:00
abstract::Osmium tetroxide complexes with nitrogen ligands (Os,L) have been widely used as probes of the DNA structure. A monoclonal antibody OsBP7H8 against DNA adducts with Os,L was produced in mice. OsBP7H8 does not bind to proteins or total yeast RNA modified with Os,2,2'-bipyridine (bipy) nor to the unmodified nucleic acid...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1999.10508339
更新日期:1999-08-01 00:00:00
abstract::It has been shown that the frequency versus size distribution of A and T overlapping and non-overlapping homopolymer tracts of N > 5 in D. discoideum gene flanking and intron regions are significantly greater than in coding regions(1). In the present report, we demonstrate, that a spatial periodicity exists in long A ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1994.10508099
更新日期:1994-08-01 00:00:00
abstract::Three dimensional models of NB-ARC domains in five different proteins were constructed based on the recently published crystal structure of the apoptotic protease activating factor 1, of which two are for tomato species, one each for flax, Arabidopsis, and nematode. Standard multiple sequence alignment was performed f...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2008.10507184
更新日期:2008-02-01 00:00:00
abstract::The current work presents a conformational evaluation of heparinase II (hepII) from Pedobacter heparinus, employing molecular dynamics (MD) simulations, in order to characterize the main features of the enzyme dynamics, as well as the role of the glycan and metal components on the protein scaffold. Accordingly, four s...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2013.809604
更新日期:2014-01-01 00:00:00
abstract::The (+) anti isomer of benz[a]pyrene diol epoxide (BPDE), 7 beta, 8 alpha-dihydroxy-9 alpha, 10 alpha-epoxy-7,8,9,10-tetrahydrobenz [a] pyrene has been identified as the probable tumorigenic lesion in mammalian systems. It forms a predominant adduct with DNA at N2 of guanine. In order to elucidate its conformation in ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1983.10507492
更新日期:1983-12-01 00:00:00
abstract::The adsorption behavior of Anastrozole (ANA) and Melphalan (MEL) anticancer drugs on the surface of silicene nanosheet (SNS) and functionalized SNS with folic acid (FA-SNS) is investigated and compared using the density functional theory (DFT) and molecular dynamics (MD) simulation. The DFT calculation is performed at...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1772881
更新日期:2020-06-05 00:00:00
abstract::Linezolid, one of the reserve antibiotic of oxazolidinone class has wide range of antimicrobial activity. Here we have conducted a fundamental study concerning the dynamics of its interaction with bovine serum albumin (BSA), and the post binding modification of the later by employing different spectroscopic (absorptio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1278721
更新日期:2018-02-01 00:00:00
abstract::Partial proteolysis of the lambda cI repressor has been carried out systematically with trypsin, chymotrypsin, elastase, endoproteinase Glu-C, kallikrein, and thrombin. The cleavage sites have been determined by (i) comparison of fragments produced and observed in SDS-polyacrylamide gel with known fragments and plots ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2008.10507249
更新日期:2008-12-01 00:00:00
abstract::Lymphatic filariasis is a debilitating vector borne parasitic disease that infects human lymphatic system by nematode Brugia malayi. Currently available anti-filarial drugs are effective only on the larval stages of parasite. So far, no effective drugs are available for humans to treat filarial infections. In this reg...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1427633
更新日期:2019-02-01 00:00:00
abstract::The With-No-Lysine (WNK) kinase family plays a significant role in regulating cation-chloride cotransporters, blood pressure and body fluid homeostasis. Mutations in the gene of WNK family, especially in WNK1 and WNK4 are responsible for pseudohypoaldosteronism type II (PHAII), characterized by hypertension. The selec...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1602079
更新日期:2020-03-01 00:00:00
abstract::Over the years the structural properties of nucleic acids have been of interest, providing data that may be of importance for DNA and RNA organization and function in the cell. We have attempted to look for the formation of parallel RNA-RNA duplexes in vitro. RNA molecules comprising complementary in the same polarity...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1995.10508860
更新日期:1995-12-01 00:00:00
abstract::Over the last few years, some novel researches in the field of medical science made a tendency to have a therapy without any complications or side-effects of the disease with the aid of prognosis about the behaviors of the substructure living biological cell. Regarding this issue, nonlinear frequency characteristics o...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1751297
更新日期:2020-04-17 00:00:00
abstract::During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promo...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.990925
更新日期:2015-01-01 00:00:00
abstract::The purpose of this study was to investigate the site-selective binding of erlotinib hydrochloride (ET), a targeted anticancer drug, to bovine serum albumin (BSA) through 1H NMR, spectroscopic, thermodynamic, and molecular modeling methods. The fluorescence quenching of BSA by ET was a result of the formation of BSA-E...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.726532
更新日期:2013-10-01 00:00:00
abstract::Within the five classes (α, β, γ, δ, and ζ) of carbonic anhydrases (CAs) the first two, containing mammal and plant representatives, are the most studied among all CAs. In this study, we have focused our investigation on the beta-class carbonic anhydrase of Methanobacterium thermoautotrophicum. We investigated both th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1025100
更新日期:2016-01-01 00:00:00
abstract::2019 - Novel Coronavirus (2019-nCOV), enclosed large genome positive-sense RNA virus characterized by crown-like spikes that protrude from their surface, and have a distinctive replication strategy. The 2019-nCOV belongs to the Coronaviridae family, principally consists of virulent pathogens showing zoonotic property,...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1781694
更新日期:2020-06-22 00:00:00
abstract::Ornithine decarboxylase (ODC) is an enzyme that initiates polyamine synthesis in human. Polyamines play key roles in cell-cell adhesion, cell motility and cell cycle regulation. Higher synthesis of polyamines also occurs in rapidly proliferating cancer cells are mediated by ODC. As per earlier studies, di-flouro-methy...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1439772
更新日期:2019-02-01 00:00:00
abstract::The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2002.10506801
更新日期:2002-06-01 00:00:00
abstract::Thermodynamic parameters of coaxial stacking at complementary helix-helix interfaces GX*pYG/CZVC (X,Y=A,C,T,G;*-nick) created by contiguous oligonucleotide hybridization were determined. The data obtained were compared to the thermodynamic parameters of coaxial stacking at the interfaces CX*pYC/GZVG. Multiple linear r...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2003.10506940
更新日期:2003-12-01 00:00:00
abstract::Calcium Dependent Protein Kinases are found in the Apicomplexan, algae, and plants; however, they are not reported in vertebrates and are regarded as excellent drug targets for pharmaceutical interventions. Calcium Dependent Protein Kinases of Cryptosporidium are probably involved in the regulation of invasion and egr...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1790036
更新日期:2020-07-07 00:00:00